Combinatorial chemistry is an exciting new development in the field of medicinal chemistry. It seeks to produce a large, synthetic compound pool through the connection of a set of different "building blocks". Through this large and diverse collection of molecules, it is hoped that better leads for new drugs can be found at much higher speed. In practice, although combinational chemistry is capable of making an enormously large number of molecules, it is impossible to actually test and isolate all of them. Thus careful decisions have to be made to select only a small number of "building blocks". Using program suite DOCK to dock all possible combinations, which is usually in the range of billions, is impossibly time-consuming and tedious. We have therefore developed a new method to attack this problem. With this method, which has been implemented into the DOCK suite, scores for all fragments are evaluated at once and combinatorial explosion is avoided by essentially transforming N1 * N2 * N3 to N1 + N2 + N3. We have applied this approach to the design of a library for cathepsin D. Our collaborator in Don Ellman's group at the University of California at Berkeley is now in the process of carrying out the experiment.